Selected Published Works Using IP2

  • Ma J, et.al., Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides, Anal Chem. 2016 Apr 5;88(7):3967-75
  • Magdeldin S, et. al., Comprehensive data analysis of human ureter proteome, Data Brief. 2016 Feb 3;6:853-7
  • Savas JN, Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis, Methods Mol Biol. 2016;1410:293-304
  • Kim TK, Tirloni L, Pinto AF, Moresco J, Yates JR 3rd, da Silva Vaz I Jr, Mulenga A, Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding, PLoS Negl Trop Dis. 2016 Jan 11
  • Pankow S, et.al. F508 CFTR interactome remodelling promotes rescue of cystic fibrosis, Nature. 2015 Dec 24;528(7583):510-6
  • Brown KJ, Seol H, Pillai DK, Sankoorikal BJ, Formolo CA, Mac J, Edwards NJ, Rose MC, Hathout Y., The human secretome atlas initiative: implications in health and disease conditions, Biochim Biophys Acta. 2013 Nov;1834(11):2454-61
  • Rayavarapu S, Coley W, Van der Meulen JH, Cakir E, Tappeta K, Kinder TB, Dillingham B, Brown KJ, Hathout Y, Nagaraju K., Activation of the ubiquitin proteasome pathway in a mouse model of inflammatory myopathy: A potential therapeutic target, Arthritis Rheum. 2013 Sep 10
  • Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR 3rd, Hetzer MW, Identification of long-lived proteins reveals exceptional stability of essential cellular structures, Cell. 2013 Aug 29;154(5):971-82
  • Butko MT, Savas JN, Friedman B, Delahunty C, Ebner F, Yates JR 3rd, Tsien RY, In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation, Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E726-35
  • Paolo Mita, Jeffrey N. Savas, Susan Ha, Nabil Djouder, John R. Yates III, Susan K. Logan, Analysis of URI Nuclear Interaction with RPB5 and Components of the R2TP/Prefoldin-Like Complex, PLoS One. 2013 May 8;8(5):e63879
  • Fonslow BR, Niessen SM, Singh M, Wong CC, Xu T, Carvalho PC, Choi J, Park SK, Yates JR 3rd. Single-Step Inline Hydroxyapatite Enrichment Facilitates Identification and Quantitation of Phosphopeptides from Mass-Limited Proteomes with MudPIT. J Proteome Res. 2012 May 4;11(5):2697-709. Link
  • Culver BP, Savas JN, Park SK, Choi JH, Zheng S, Zeitlin SO, Yates JR 3rd, Tanese N. Proteomic analysis of wild-type and mutant huntingtin associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis. J Biol Chem., May 3, 2012 Link
  • Lale Ozcan, Catherine C.L. Wong, Gang Li, Tao Xu, Utpal Pajvani, Sung Kyu Robin Park, Anetta Wronska, Bi-Xing Chen, Andrew R. Marks, Akiyoshi Fukamizu, Johannes Backs, Harold A. Singer, John R. Yates, Domenico Accili, Ira Tabas. Calcium Signaling through CaMKII Regulates Hepatic Glucose Production in Fasting and Obesity. Cell Metabolism, April 12, 2012 Link
  • Sinnamon JR, Waddell CB, Nik S, Chen EI, Czaplinski K., Hnrpab regulates neural development and neuron cell survival after glutamate stimulation. RNA. Feb 13, 2012; Published Online February 13 2012 Link
  • Savas JN, Toyama BH, Xu T, Yates III JR, Hetzer MW., Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain. Science. February 2 2012; Published Online February 2, 2012 Link
  • Jeong H, Cohen DE, Cui L, Supinski A, Savas JN, Mazzulli JR, Yates III JR, Bordone L, Guarente L, Krainc D., Sirt1 mediates neuroprotection from mutant huntingtin by activation of the TORC1 and CREB transcriptional pathway. Nature Medicine. Dec 18, 2011; 18(1):159-65 Link
  • Keck JM, Jones MH, Wong CC, Binkley J, Chen D, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates 3rd JR, Winey M., A cell cycle phosphoproteome of the yeast centrosome. Science. 2011 Jun 24;332(6037):1557-61 Link
  • Zhang A, Williamson CD, Wong DS, Bullough MD, Brown KJ, Hathout Y, Colberg-Poley AM, Quantitative Proteomic Analyses of Human Cytomegalovirus-Induced Restructuring of Endoplasmic Reticulum-Mitochondrial Contacts at Late Times of Infection. Mol Cell Proteomics. 2011 Oct;10(10):M111.009936. Epub 2011 Jul 8 Link

Proteomics Software Tools Integrated into the IP2

  • Park, S. K., Venable, J. D., Xu, T., Yates, J. R., 3rd. A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods, 5, (4), 319-22 (2008)Link
  • Lu B, Ruse C, Xu T, Park SK, Yates J 3rd., Automatic validation of phosphopeptide identifications from tandem mass spectra, Anal Chem. 2007 Feb 15;79(4):1301-10 Link
  • Cociorva D, Tabb DL, Yates JR., III Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect. Curr Protocols Bioinformatics. 2007 Jan; Chapter 13(Unit 13.4) Link
  • Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J. & Gygi, S. P. (2006). A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24, 1285-1292 Link
  • Xu, T., Venable, J. D., Park, S. K., Cociorva, D., Lu, B., Liao, L., Wohlschlegel, J., Hewel, J., Yates, J. R. I. ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program, Mol Cell Proteomics, 5, S174 (2006) Link
  • McDonald W. H., Tabb D. L., Sadygov R. G., MacCoss M. J., Venable J., Graumann J., Johnson J. R., Cociorva D., Yates J. R., 3rd (2004) MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass. Spectrom. 18, 2162–2168 Link
  • Tabb DL, McDonald WH, Yates JR 3rd., DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics, J Proteome Res. 2002 Jan-Feb;1(1):21-6. Link
  • Eng, J. K.; McCormack, A. L.; Yates, J. R., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 1994, 5, 976-989 Link